scholarly journals Highly mobile DNA segment of IncI alpha plasmid R64: a clustered inversion region.

1986 ◽  
Vol 165 (1) ◽  
pp. 94-100 ◽  
Author(s):  
T Komano ◽  
A Kubo ◽  
T Kayanuma ◽  
T Furuichi ◽  
T Nisioka
Keyword(s):  
Mobile Dna ◽  
Inversion Region ◽  
Plasmid R64

scholarly journals TBP and SNAP50 transcription factors bind specifically to the Pr77 promoter sequence from trypanosomatid non-LTR retrotransposons

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Francisco Macías ◽  
Raquel Afonso-Lehmann ◽  
Patricia E. Carreira ◽  
M. Carmen Thomas
Keyword(s):  
Transcription Factors ◽  
Protein Interactions ◽  
Dna Sequences ◽  
Direct Interaction ◽  
Promoter Sequence ◽  
Nuclear Proteins ◽  
Hill Coefficient ◽  
Small Nuclear Rna ◽  
Mobile Dna ◽  
Mobility Shift

Abstract Background Trypanosomatid genomes are colonized by active and inactive mobile DNA elements, such as LINE, SINE-like, SIDER and DIRE retrotransposons. These elements all share a 77-nucleotide-long sequence at their 5′ ends, known as Pr77, which activates transcription, thereby generating abundant unspliced and translatable transcripts. However, transcription factors that mediates this process have still not been reported. Methods TATA-binding protein (TBP) and small nuclear RNA-activating protein 50 kDa (SNAP50) recombinant proteins and specific antibodies raised against them were generated. Protein capture assay, electrophoretic mobility-shift assays (EMSA) and EMSA competition assays carried out using these proteins and nuclear proteins of the parasite together to specific DNA sequences used as probes allowed detecting direct interaction of these transcription factors to Pr77 sequence. Results This study identified TBP and SNAP50 as part of the DNA-protein complex formed by the Pr77 promoter sequence and nuclear proteins of Trypanosoma cruzi. TBP establishes direct and specific contact with the Pr77 sequence, where the DPE and DPE downstream regions are docking sites with preferential binding. TBP binds cooperatively (Hill coefficient = 1.67) to Pr77 and to both strands of the Pr77 sequence, while the conformation of this highly structured sequence is not involved in TBP binding. Direct binding of SNAP50 to the Pr77 sequence is weak and may be mediated by protein–protein interactions through other trypanosomatid nuclear proteins. Conclusions Identification of the transcription factors that mediate Pr77 transcription may help to elucidate how these retrotransposons are mobilized within the trypanosomatid genomes and their roles in gene regulation processes in this human parasite. Graphic abstract

scholarly journals Multidrug-Resistant Enterococci Lack CRISPR-cas

mBio ◽  
2010 ◽  
Vol 1 (4) ◽  
Author(s):  
Kelli L. Palmer ◽  
Michael S. Gilmore
Keyword(s):  
Antibiotic Resistance ◽  
Draft Genome ◽  
Inverse Correlation ◽  
Multidrug Resistant ◽  
Mobile Elements ◽  
Mobile Dna ◽  
Data Set ◽  
Content Type ◽  
Genome Defense ◽  
Acquired Antibiotic Resistance

ABSTRACT Clustered, regularly interspaced short palindromic repeats (CRISPR) provide bacteria and archaea with sequence-specific, acquired defense against plasmids and phage. Because mobile elements constitute up to 25% of the genome of multidrug-resistant (MDR) enterococci, it was of interest to examine the codistribution of CRISPR and acquired antibiotic resistance in enterococcal lineages. A database was built from 16 Enterococcus faecalis draft genome sequences to identify commonalities and polymorphisms in the location and content of CRISPR loci. With this data set, we were able to detect identities between CRISPR spacers and sequences from mobile elements, including pheromone-responsive plasmids and phage, suggesting that CRISPR regulates the flux of these elements through the E. faecalis species. Based on conserved locations of CRISPR and CRISPR-cas loci and the discovery of a new CRISPR locus with associated functional genes, CRISPR3-cas, we screened additional E. faecalis strains for CRISPR content, including isolates predating the use of antibiotics. We found a highly significant inverse correlation between the presence of a CRISPR-cas locus and acquired antibiotic resistance in E. faecalis, and examination of an additional eight E. faecium genomes yielded similar results for that species. A mechanism for CRISPR-cas loss in E. faecalis was identified. The inverse relationship between CRISPR-cas and antibiotic resistance suggests that antibiotic use inadvertently selects for enterococcal strains with compromised genome defense. IMPORTANCE For many bacteria, including the opportunistically pathogenic enterococci, antibiotic resistance is mediated by acquisition of new DNA and is frequently encoded on mobile DNA elements such as plasmids and transposons. Certain enterococcal lineages have recently emerged that are characterized by abundant mobile DNA, including numerous viruses (phage), and plasmids and transposons encoding multiple antibiotic resistances. These lineages cause hospital infection outbreaks around the world. The striking influx of mobile DNA into these lineages is in contrast to what would be expected if a self (genome)-defense system was present. Clustered, regularly interspaced short palindromic repeat (CRISPR) defense is a recently discovered mechanism of prokaryotic self-defense that provides a type of acquired immunity. Here, we find that antibiotic resistance and possession of complete CRISPR loci are inversely related and that members of recently emerged high-risk enterococcal lineages lack complete CRISPR loci. Our results suggest that antibiotic therapy inadvertently selects for enterococci with compromised genome defense.

Effect of Shear and Water Cut on Phase Inversion and Droplet Size Distribution in Oil–Water Flow

2018 ◽  
Vol 141 (3) ◽  
Author(s):  
Mo Zhang ◽  
Ramin Dabirian ◽  
Ram S. Mohan ◽  
Ovadia Shoham
Keyword(s):  
Size Distribution ◽  
Droplet Size ◽  
Phase Inversion ◽  
Droplet Size Distribution ◽  
Continuous Phase ◽  
Dispersed Phase ◽  
Water Emulsion ◽  
Inversion Region ◽  
Oil Water ◽  
Water Cut

Oil–water dispersed flow occurs commonly in the petroleum industry during the production and transportation of crudes. Phase inversion occurs when the dispersed phase grows into the continuous phase and the continuous phase becomes the dispersed phase caused by changes in the composition, interfacial properties, and other factors. Production equipment, such as pumps and chokes, generates shear in oil–water mixture flow, which has a strong effect on phase inversion phenomena. The objective of this paper is to investigate the effects of shear intensity and water cut (WC) on the phase inversion region and also the droplet size distribution. A state-of-the-art closed-loop two phase (oil–water) flow facility including a multipass gear pump and a differential dielectric sensor (DDS) is used to identify the phase inversion region. Also, the facility utilizes an in-line droplet size analyzer (a high speed camera), to record real-time videos of oil–water emulsion to determine the droplet size distribution. The experimental data for phase inversion confirm that as shear intensity increases, the phase inversion occurs at relatively higher dispersed phase fractions. Also the data show that oil-in-water emulsion requires larger dispersed phase volumetric fraction for phase inversion as compared with that of water-in-oil emulsion under the same shear intensity conditions. Experiments for droplet size distribution confirm that larger droplets are obtained for the water continuous phase, and increasing the dispersed phase volume fraction leads to the creation of larger droplets.

scholarly journals Mobile DNA and evolution in the 21st century

Mobile DNA ◽  
2010 ◽  
Vol 1 (1) ◽  
pp. 4 ◽  
Author(s):  
James A Shapiro
Keyword(s):  
21St Century ◽  
Mobile Dna

Mobile DNA: Mechanisms, Utility, and Consequences

2014 ◽  
pp. 1-23
Author(s):  
Adam R. Parks ◽  
Joseph E. Peters
Keyword(s):  
Mobile Dna

scholarly journals A Novel and Direct Metamobilome Approach improves the Detection of Larger-sized Circular Elements across Kingdoms

2019 ◽  
Author(s):  
Katrine Skov Alanin ◽  
Tue Sparholt Jørgensen ◽  
Patrick Browne ◽  
Bent Petersen ◽  
Leise Riber ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Bacterial Species ◽  
Human Health Risk ◽  
Prokaryotic Genome ◽  
Mobile Genetic Elements ◽  
Wastewater Sample ◽  
Mobile Dna ◽  
Complex Samples ◽  
Genetic Elements ◽  
Dna Elements

AbstractMobile genetic elements (MGEs) are instrumental in natural prokaryotic genome editing, permitting genome plasticity and allowing microbes to accumulate immense genetic diversity. MGEs include DNA elements such as plasmids, transposons and Insertion Sequences (IS-elements), as well as bacteriophages (phages), and they serve as a vast communal gene pool. These mobile DNA elements represent a human health risk as they can add new traits, such as antibiotic resistance or virulence, to a bacterial strain. Sequencing libraries targeting circular MGEs, referred to as mobilomes, allows the expansion of our current understanding of the mechanisms behind the mobility, prevalence and content of these elements. However, metamobilomes from bacterial communities are not studied to the same extent as metagenomics, partly because of methodological biases arising from multiple displacement amplification (MDA), often used in previous metamobilome publications. In this study, we show that MDA is detrimental to the detection of larger-sized plasmids if small plasmids are present by comparing the abundances of reads mapping to plasmids in a wastewater sample spiked with a mock community of selected plasmids with and without MDA. Furthermore, we show that it is possible to produce samples consisting almost exclusively of circular MGEs and obtain a catalog of larger, complete, circular MGEs from complex samples without the use of MDA.ImportanceMobile genetic elements (MGEs) can transport genetic information between genomes in different bacterial species, adding new traits, potentially generating dangerous multidrug-resistant pathogens. In fact, plasmids and circular MGEs can encode bacterial genetic specializations such as virulence, resistance to metals, antimicrobial compounds, and bacteriophages, as well as the degradation of xenobiotics. For this reason, circular MGEs are crucial to investigate, but they are often missed in metagenomics and ecological studies. In this study, we present, for the first time, an improved method, which reduces the bias towards small MGEs and we demonstrate that this method can unveil larger, complete circular MGEs from complex samples without the use of multiple displacement amplification. This method may result in the detection of larger-sized plasmids that have hitherto remained unnoticed and therefore has the potential to reveal novel accessory genes, acting as possible targets in the development of preventive strategies directed at pathogens.

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